Various, chemical, biological, and other substances or materials can be incorporated into beads. If collections of such beads can be stored and retrieved with an automated or robotic handling system, customers wishing to obtain those beads can receive the bead types they want from inventory at reasonable cost, and in a potentially short delivery time. Previous bead handling systems stored inventory beads in multiple capsules, one for each bead type, with each capsule containing a pre-loaded number of beads. If the beads were subsequently dispensed into titer plates or trays, for example at a rate of one bead per well, then the number of beads per capsule would dictate a minimum number of plates or lot size that the customer would be required to purchase. Some customers, however, may only wish to purchase one plate while others may desire hundreds or more. Establishing a minimum plate purchase can force some customers to buy more plates than they need, inefficiently raising the cost. In addition, when inventory beads are stored in capsule format, the number of beads contained in a capsule can be less than some ordered quantities, requiring multiple capsule retrievals to extract the necessary beads and fill the order, increasing retrieval time and cost. In addition, when beads are dispensed to a plate at a rate of one bead per well or multiple beads per well, the concentration of the oligonucleotide or other materials embedded in the beads can vary, leading to differences in oligonucleotide concentrations when the beads are used. Other problems in existing bead handling and dispensing systems exist.